Magnesium in PDB 8yzx: Sesquiterpene Synthase Syda

The structure of Sesquiterpene Synthase Syda, PDB code: 8yzx was solved by A.Fan, S.Fan, M.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.92 / 3.80
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.928, 157.928, 224.841, 90, 90, 90
R / Rfree (%)	17.9 / 21.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Sesquiterpene Synthase Syda (pdb code 8yzx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Sesquiterpene Synthase Syda, PDB code: 8yzx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:79.0 occ:1.00 O2 A:POP401 2.1 71.5 1.0 OD1 A:ASP99 2.2 84.2 1.0 OE2 A:GLU163 2.5 116.6 1.0 CG A:ASP99 3.2 90.5 1.0 CD A:GLU163 3.4 105.1 1.0 P1 A:POP401 3.5 89.9 1.0 OE1 A:GLU163 3.7 100.0 1.0 OD2 A:ASP99 3.8 75.3 1.0 O A:THR185 3.9 74.7 1.0 CB A:THR185 4.0 84.4 1.0 O3 A:POP401 4.0 87.0 1.0 CE1 A:PHE156 4.0 99.6 1.0 OG1 A:THR160 4.2 64.6 1.0 CG2 A:THR160 4.3 93.7 1.0 O1 A:POP401 4.3 94.8 1.0 CB A:ASP99 4.3 81.3 1.0 O A:POP401 4.5 76.3 1.0 CD1 A:PHE156 4.6 98.3 1.0 CG2 A:THR185 4.6 93.3 1.0 CA A:THR185 4.7 89.2 1.0 C A:THR185 4.7 82.1 1.0 OG1 A:THR185 4.7 67.8 1.0 CB A:THR160 4.7 80.8 1.0 CG A:GLU163 4.8 82.7 1.0 MG A:MG403 4.9 74.2 1.0 NH1 A:ARG182 5.0 94.6 1.0 CA A:ASP99 5.0 83.3 1.0

Magnesium binding site 2 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:74.2 occ:1.00 OD2 A:ASP99 2.0 75.3 1.0 O4 A:POP401 2.9 95.5 1.0 O1 A:POP401 3.0 94.8 1.0 CG A:ASP99 3.1 90.5 1.0 O A:POP401 3.5 76.3 1.0 NZ A:LYS232 3.5 87.5 1.0 P2 A:POP401 3.5 80.9 1.0 P1 A:POP401 3.5 89.9 1.0 O2 A:POP401 3.5 71.5 1.0 O6 A:POP401 3.6 80.0 1.0 OD1 A:ASP99 3.7 84.2 1.0 OE1 A:GLU239 4.0 105.1 1.0 NH2 A:ARG304 4.1 87.7 1.0 O A:ASP99 4.1 104.5 1.0 OE2 A:GLU100 4.2 94.9 1.0 CB A:ASP99 4.3 81.3 1.0 CE A:LYS232 4.4 89.8 1.0 OE1 A:GLU233 4.6 87.7 1.0 C A:ASP99 4.8 97.1 1.0 OE2 A:GLU239 4.8 110.7 1.0 CD A:GLU239 4.9 109.7 1.0 CD A:GLU100 4.9 101.5 1.0 MG A:MG402 4.9 79.0 1.0 O5 A:POP401 5.0 80.9 1.0 O3 A:POP401 5.0 87.0 1.0

Magnesium binding site 3 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:52.5 occ:1.00 OD1 A:ASN225 2.0 83.9 1.0 OE2 A:GLU233 2.6 104.3 1.0 OE1 A:GLU233 2.7 87.7 1.0 OG A:SER229 2.8 109.8 1.0 O1 A:POP401 2.9 94.8 1.0 CG A:ASN225 3.0 90.1 1.0 CD A:GLU233 3.0 95.5 1.0 O3 A:POP401 3.3 87.0 1.0 O4 A:POP401 3.3 95.5 1.0 O5 A:POP401 3.5 80.9 1.0 P1 A:POP401 3.6 89.9 1.0 ND2 A:ASN225 3.6 83.7 1.0 OD1 A:ASP226 3.7 91.2 1.0 NH2 A:ARG182 3.8 89.2 1.0 P2 A:POP401 3.8 80.9 1.0 O A:ASN225 3.8 98.7 1.0 C A:ASN225 4.0 93.2 1.0 O A:POP401 4.0 76.3 1.0 CB A:SER229 4.1 109.7 1.0 N A:ASP226 4.1 93.7 1.0 CA A:ASP226 4.2 99.0 1.0 CB A:ASN225 4.2 87.6 1.0 NH1 A:ARG182 4.3 94.6 1.0 CZ A:ARG182 4.3 86.3 1.0 CG A:ASP226 4.5 93.7 1.0 CG A:GLU233 4.5 90.6 1.0 ND2 A:ASN242 4.6 92.2 1.0 CA A:ASN225 4.7 74.7 1.0 CB A:ASN242 4.8 93.1 1.0 OE2 A:GLU239 4.8 110.7 1.0 O2 A:POP401 5.0 71.5 1.0 CB A:ASP226 5.0 92.2 1.0

Magnesium binding site 4 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:91.6 occ:1.00 OD2 B:ASP99 2.2 94.0 1.0 O4 B:POP401 2.6 142.8 1.0 O5 B:POP401 2.9 89.4 1.0 CG B:ASP99 3.0 100.7 1.0 O3 B:POP401 3.0 123.4 1.0 OD1 B:ASP99 3.1 105.3 1.0 P2 B:POP401 3.2 118.2 1.0 OE1 B:GLU239 3.6 121.9 1.0 OE2 B:GLU239 3.6 89.7 1.0 OE2 B:GLU163 3.9 108.8 1.0 P1 B:POP401 3.9 106.1 1.0 CD B:GLU239 4.0 107.4 1.0 MG B:MG404 4.0 82.9 1.0 O1 B:POP401 4.0 98.5 1.0 O B:POP401 4.0 110.3 1.0 O B:ASP99 4.0 124.7 1.0 NZ B:LYS232 4.1 100.0 1.0 OE1 B:GLU163 4.3 110.5 1.0 MG B:MG403 4.4 79.7 1.0 CB B:ASP99 4.4 78.0 1.0 CD B:GLU163 4.5 112.2 1.0 O6 B:POP401 4.6 89.5 1.0 OE1 B:GLU233 4.6 94.8 1.0 NH2 B:ARG304 4.9 159.5 1.0 C B:ASP99 4.9 106.7 1.0 CA B:ASP99 5.0 88.1 1.0

Magnesium binding site 5 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:79.7 occ:1.00 OD1 B:ASN225 2.0 94.8 1.0 O3 B:POP401 2.4 123.4 1.0 O5 B:POP401 2.8 89.4 1.0 OE1 B:GLU233 2.8 94.8 1.0 CG B:ASN225 3.1 94.9 1.0 P1 B:POP401 3.2 106.1 1.0 O B:POP401 3.3 110.3 1.0 O2 B:POP401 3.4 88.6 1.0 OE2 B:GLU233 3.4 101.0 1.0 CD B:GLU233 3.5 100.6 1.0 O B:ASN225 3.6 98.6 1.0 OG B:SER229 3.6 97.0 1.0 P2 B:POP401 3.6 118.2 1.0 ND2 B:ASN225 3.6 95.3 1.0 NH2 B:ARG182 3.8 98.9 1.0 NH1 B:ARG182 3.9 101.4 1.0 CZ B:ARG182 4.1 96.0 1.0 CB B:ASN225 4.4 83.8 1.0 MG B:MG402 4.4 91.6 1.0 C B:ASN225 4.4 105.1 1.0 OD1 B:ASP226 4.5 87.3 1.0 OE2 B:GLU239 4.5 89.7 1.0 O1 B:POP401 4.6 98.5 1.0 O6 B:POP401 4.6 89.5 1.0 OE1 B:GLU239 4.6 121.9 1.0 O4 B:POP401 4.7 142.8 1.0 CB B:SER229 4.8 106.5 1.0 CB B:ASN242 4.9 92.1 1.0 CD B:GLU239 4.9 107.4 1.0 CG B:GLU233 5.0 113.2 1.0

Magnesium binding site 6 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:82.9 occ:1.00 OD1 B:ASP99 2.1 105.3 1.0 O6 B:POP401 3.0 89.5 1.0 O4 B:POP401 3.0 142.8 1.0 OE1 B:GLU163 3.0 110.5 1.0 O5 B:POP401 3.1 89.4 1.0 P2 B:POP401 3.2 118.2 1.0 OE2 B:GLU163 3.2 108.8 1.0 CD B:GLU163 3.3 112.2 1.0 CG B:ASP99 3.3 100.7 1.0 CB B:THR185 3.7 82.0 1.0 O B:THR185 3.8 71.8 1.0 OG1 B:THR160 3.8 77.8 1.0 OD2 B:ASP99 4.0 94.0 1.0 MG B:MG402 4.0 91.6 1.0 CE1 B:PHE156 4.2 81.0 1.0 CG2 B:THR185 4.4 91.5 1.0 CB B:ASP99 4.4 78.0 1.0 CG B:GLU163 4.5 105.5 1.0 CA B:THR185 4.5 83.7 1.0 OG1 B:THR185 4.5 77.7 1.0 C B:THR185 4.5 71.9 1.0 CG2 B:THR160 4.5 83.5 1.0 CB B:THR160 4.6 82.1 1.0 O B:POP401 4.8 110.3 1.0 CA B:THR160 4.8 83.9 1.0 CD1 B:PHE156 4.9 90.0 1.0 NH1 B:ARG182 4.9 101.4 1.0

Magnesium binding site 7 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:77.7 occ:1.00 O5 C:POP401 2.3 97.4 1.0 OG C:SER229 2.7 73.6 1.0 OE2 C:GLU233 2.7 93.8 1.0 OD1 C:ASN225 2.7 109.0 1.0 O C:POP401 2.8 87.8 1.0 P2 C:POP401 2.9 143.0 1.0 OE1 C:GLU233 3.1 91.2 1.0 O4 C:POP401 3.2 110.1 1.0 CD C:GLU233 3.2 94.7 1.0 O C:HOH501 3.3 86.8 1.0 CG C:ASN225 3.6 100.5 1.0 CB C:SER229 3.7 95.1 1.0 ND2 C:ASN225 3.8 96.4 1.0 OD1 C:ASP226 4.0 84.1 1.0 O C:ASN225 4.1 90.3 1.0 P1 C:POP401 4.1 102.1 1.0 NH2 C:ARG182 4.3 100.0 1.0 O3 C:POP401 4.3 96.3 1.0 O C:HOH502 4.3 94.6 1.0 O6 C:POP401 4.3 53.5 1.0 CA C:ASP226 4.4 90.9 1.0 C C:ASN225 4.5 92.0 1.0 CZ C:ARG182 4.6 97.6 1.0 N C:ASP226 4.6 92.6 1.0 NH1 C:ARG182 4.6 99.4 1.0 CG C:ASP226 4.7 87.0 1.0 O1 C:POP401 4.7 77.9 1.0 CG C:GLU233 4.7 97.6 1.0 CB C:ASN242 4.9 84.5 1.0 CB C:ASN225 4.9 98.1 1.0

Magnesium binding site 8 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:87.1 occ:1.00 O C:HOH506 2.0 82.7 1.0 OD1 C:ASP99 2.2 99.3 1.0 O C:HOH503 2.4 105.4 1.0 O C:HOH504 2.7 77.0 1.0 OE1 C:GLU163 2.9 95.2 1.0 O3 C:POP401 2.9 96.3 1.0 CG C:ASP99 2.9 94.7 1.0 OD2 C:ASP99 3.0 83.1 1.0 O1 C:POP401 3.1 77.9 1.0 OE2 C:GLU163 3.4 99.2 1.0 P1 C:POP401 3.5 102.1 1.0 CD C:GLU163 3.5 95.9 1.0 O2 C:POP401 4.0 128.0 1.0 O C:HOH502 4.0 94.6 1.0 CG2 C:THR160 4.3 92.3 1.0 MG C:MG404 4.3 77.8 1.0 CB C:ASP99 4.4 93.1 1.0 O C:ASP99 4.8 101.1 1.0 OG1 C:THR160 4.8 84.4 1.0 CA C:ASP99 4.9 91.3 1.0 O C:POP401 5.0 87.8 1.0

Magnesium binding site 9 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:77.8 occ:1.00 O C:HOH505 2.0 105.9 1.0 O3 C:POP401 2.2 96.3 1.0 OD2 C:ASP99 2.5 83.1 1.0 O2 C:POP401 2.7 128.0 1.0 O6 C:POP401 2.7 53.5 1.0 P1 C:POP401 2.9 102.1 1.0 O C:HOH502 3.0 94.6 1.0 NZ C:LYS232 3.3 106.4 1.0 NH2 C:ARG304 3.4 103.5 1.0 P2 C:POP401 3.5 143.0 1.0 O C:POP401 3.6 87.8 1.0 O5 C:POP401 3.6 97.4 1.0 CG C:ASP99 3.7 94.7 1.0 O1 C:POP401 4.2 77.9 1.0 MG C:MG403 4.3 87.1 1.0 OD1 C:ASP99 4.4 99.3 1.0 OE2 C:GLU100 4.4 98.3 1.0 CZ C:ARG304 4.4 97.4 1.0 CE C:LYS232 4.5 93.6 1.0 CB C:ASP99 4.6 93.1 1.0 OE1 C:GLU233 4.7 91.2 1.0 O4 C:POP401 4.9 110.1 1.0 O C:HOH503 4.9 105.4 1.0 OE1 C:GLU239 4.9 111.0 1.0

Magnesium binding site 10 out of 12 in the Sesquiterpene Synthase Syda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Sesquiterpene Synthase Syda within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:64.9 occ:1.00 O6 D:POP401 2.2 102.9 1.0 OD1 D:ASP99 2.2 104.3 1.0 OE2 D:GLU163 2.8 101.1 1.0 P2 D:POP401 3.2 111.8 1.0 CG D:ASP99 3.2 95.2 1.0 O4 D:POP401 3.3 94.7 1.0 MG D:MG403 3.5 75.1 1.0 OD2 D:ASP99 3.7 86.6 1.0 O D:THR185 3.7 83.8 1.0 O5 D:POP401 3.7 108.0 1.0 CD D:GLU163 3.7 104.6 1.0 CB D:THR185 4.0 79.8 1.0 OG1 D:THR160 4.0 87.5 1.0 OE1 D:GLU163 4.1 105.5 1.0 CE1 D:PHE156 4.1 95.0 1.0 CB D:ASP99 4.4 86.9 1.0 C D:THR185 4.5 79.3 1.0 NH1 D:ARG182 4.6 109.1 1.0 O D:POP401 4.6 92.6 1.0 CA D:THR185 4.6 78.6 1.0 CG2 D:THR185 4.7 95.3 1.0 OG1 D:THR185 4.8 64.6 1.0 CZ D:PHE156 4.8 92.2 1.0 CD1 D:PHE156 4.9 98.5 1.0 O1 D:POP401 5.0 115.0 1.0

A.Fan, S.Fan, M.Wu. Sesquiterpene Synthase Syda To Be Published.